Technical Specs

Support

Querying Pathway/Genome Databases

This page summarizes approaches to querying information in
Pathway/Genome Databases (PGDBs) maintained by Pathway Tools. Although the Pathway/Genome
Navigator graphical user interface provides a number of fixed
queries, those queries are of limited complexity. To write more
comprehensive and sophisticated queries, the user will need to
perform some amount of programming.

There are several approaches to writing programs that query PGDBs:

Write a program that uses an API (application program
interface) to dynamically query and/or edit a PGDB while it resides
within Pathway Tools. Such programs can be written in Python, Perl,
Java, and Common Lisp.

Export a PGDB to a set of flat files, and:

Use Perl or another language to parse the data in those flat files directly

Use BioWarehouse to load the flat files into another database management system (DBMS), such as
a relational DBMS, and query them there using SQL.

The next section describes the API options in more detail.

The Pathway Tools API

Please read the Pathway Tools
API document to get an overview of how to access Pathway Tools programmatically.

Pathway Tools is written in Common Lisp, so the most powerful and
recommended way to interact with Pathway Tools is via the Common Lisp
API. For programmers who are not familiar with Common Lisp, a more
limited set of functionality is available using Perl or Java.

GFP -- the Generic Frame Protocol -- is the API for querying the
object database underlying Pathway Tools DBs. The documentation below
describes the Lisp interface, but translations also exist for Perl and
Java.